<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01//EN" "http://www.w3.org/TR/html4/strict.dtd">
<html>
<head>
<meta http-equiv="Content-Type" content="application/xhtml+xml; charset=UTF-8" />
<title>GenomeTools - manual page for GT-LTRDIGEST(1)</title>
<link rel="stylesheet" type="text/css" href="style.css">
<link rel="stylesheet" href="..//style.css" type="text/css" />
</head>
<body>
<div id="menu">
<ul>
<li><a href="../index.html">Overview</a></li>
<li><a href="https://github.com/genometools/genometools/releases">Releases</a></li>
<li><a href="pub/">Archive</a></li>
<li><a href="https://github.com/genometools/genometools">Browse source</a></li>
<li><a href="http://github.com/genometools/genometools/issues/">Issue tracker</a></li>
<li><a href="../documentation.html">Documentation</a></li>
  <ul class="submenu">
    <li><a id="current" href="../tools.html">Tools</a></li>
    <li><a href="../manuals.html">Manuals</a></li>
    <li><a href="../libgenometools.html">C API</a></li>
    <li><a href="../docs.html"><tt>gtscript</tt> docs</a></li>
    <li><a href="../contract.html">Development Contract</a></li>
    <li><a href="../contribute.html">Contribute</a></li>
  </ul>
<li><a href="../annotationsketch.html"><tt>AnnotationSketch</tt></a></li>
<li><a href="../cgi-bin/gff3validator.cgi">GFF3 validator</a></li>
<li><a href="../license.html">License</a></li>
</ul>
</div>
<div id="main">
<div class="sect1">
<h2 id="_name">NAME</h2>
<div class="sectionbody">
<div class="paragraph"><p>gt-ltrdigest - Identifies and annotates sequence features in LTR retrotransposon candidates.</p></div>
</div>
</div>
<div class="sect1">
<h2 id="_synopsis">SYNOPSIS</h2>
<div class="sectionbody">
<div class="paragraph"><p><strong>gt ltrdigest</strong> [option &#8230;] gff3_file</p></div>
</div>
</div>
<div class="sect1">
<h2 id="_description">DESCRIPTION</h2>
<div class="sectionbody">
<div class="dlist"><dl>
<dt class="hdlist1">
<strong>-outfileprefix</strong> [<em>string</em>]
</dt>
<dd>
<p>
prefix for output files (e.g. <em>foo</em> will create files called <em>foo_*.csv</em> and <em>foo_*.fas</em>)
Omit this option for GFF3 output only.
</p>
</dd>
<dt class="hdlist1">
<strong>-metadata</strong> [<em>yes|no</em>]
</dt>
<dd>
<p>
output metadata (run conditions) to separate file (default: yes)
</p>
</dd>
<dt class="hdlist1">
<strong>-seqnamelen</strong> [<em>value</em>]
</dt>
<dd>
<p>
set maximal length of sequence names in FASTA headers (e.g. for clustalw or similar tools) (default: 20)
</p>
</dd>
<dt class="hdlist1">
<strong>-pptlen</strong> [<em>start</em> <em>end</em>]
</dt>
<dd>
<p>
required PPT length range (default: [8..30])
</p>
</dd>
<dt class="hdlist1">
<strong>-uboxlen</strong> [<em>start</em> <em>end</em>]
</dt>
<dd>
<p>
required U-box length range (default: [3..30])
</p>
</dd>
<dt class="hdlist1">
<strong>-uboxdist</strong> [<em>value</em>]
</dt>
<dd>
<p>
allowed U-box distance range from PPT (default: 0)
</p>
</dd>
<dt class="hdlist1">
<strong>-pptradius</strong> [<em>value</em>]
</dt>
<dd>
<p>
radius around beginning of 3' LTR to search for PPT (default: 30)
</p>
</dd>
<dt class="hdlist1">
<strong>-pptrprob</strong> [<em>value</em>]
</dt>
<dd>
<p>
purine emission probability inside PPT (default: 0.970000)
</p>
</dd>
<dt class="hdlist1">
<strong>-pptyprob</strong> [<em>value</em>]
</dt>
<dd>
<p>
pyrimidine emission probability inside PPT (default: 0.030000)
</p>
</dd>
<dt class="hdlist1">
<strong>-pptgprob</strong> [<em>value</em>]
</dt>
<dd>
<p>
background G emission probability outside PPT (default: 0.250000)
</p>
</dd>
<dt class="hdlist1">
<strong>-pptcprob</strong> [<em>value</em>]
</dt>
<dd>
<p>
background C emission probability outside PPT (default: 0.250000)
</p>
</dd>
<dt class="hdlist1">
<strong>-pptaprob</strong> [<em>value</em>]
</dt>
<dd>
<p>
background A emission probability outside PPT (default: 0.250000)
</p>
</dd>
<dt class="hdlist1">
<strong>-ppttprob</strong> [<em>value</em>]
</dt>
<dd>
<p>
background T emission probability outside PPT (default: 0.250000)
</p>
</dd>
<dt class="hdlist1">
<strong>-pptuprob</strong> [<em>value</em>]
</dt>
<dd>
<p>
U/T emission probability inside U-box (default: 0.910000)
</p>
</dd>
<dt class="hdlist1">
<strong>-trnas</strong> [<em>filename</em>]
</dt>
<dd>
<p>
tRNA library in multiple FASTA format for PBS detection
Omit this option to disable PBS search.
</p>
</dd>
<dt class="hdlist1">
<strong>-pbsalilen</strong> [<em>start</em> <em>end</em>]
</dt>
<dd>
<p>
required PBS/tRNA alignment length range (default: [11..30])
</p>
</dd>
<dt class="hdlist1">
<strong>-pbsoffset</strong> [<em>start</em> <em>end</em>]
</dt>
<dd>
<p>
allowed PBS offset from LTR boundary range (default: [0..5])
</p>
</dd>
<dt class="hdlist1">
<strong>-pbstrnaoffset</strong> [<em>start</em> <em>end</em>]
</dt>
<dd>
<p>
allowed PBS/tRNA 3' end alignment offset range (default: [0..5])
</p>
</dd>
<dt class="hdlist1">
<strong>-pbsmaxedist</strong> [<em>value</em>]
</dt>
<dd>
<p>
maximal allowed PBS/tRNA alignment unit edit distance (default: 1)
</p>
</dd>
<dt class="hdlist1">
<strong>-pbsradius</strong> [<em>value</em>]
</dt>
<dd>
<p>
radius around end of 5' LTR to search for PBS (default: 30)
</p>
</dd>
<dt class="hdlist1">
<strong>-hmms</strong> 
</dt>
<dd>
<p>
profile HMM models for domain detection (separate by spaces, finish with --) in HMMER3 format
Omit this option to disable pHMM search.
</p>
</dd>
<dt class="hdlist1">
<strong>-pdomevalcutoff</strong> [<em>value</em>]
</dt>
<dd>
<p>
global E-value cutoff for pHMM search
default 1E-6
</p>
</dd>
<dt class="hdlist1">
<strong>-pdomcutoff</strong> [<em>&#8230;</em>]
</dt>
<dd>
<p>
model-specific score cutoff
choose from TC (trusted cutoff) | GA (gathering cutoff) | NONE (no cutoffs) (default: NONE)
</p>
</dd>
<dt class="hdlist1">
<strong>-aliout</strong> [<em>yes|no</em>]
</dt>
<dd>
<p>
output pHMM to amino acid sequence alignments (default: no)
</p>
</dd>
<dt class="hdlist1">
<strong>-aaout</strong> [<em>yes|no</em>]
</dt>
<dd>
<p>
output amino acid sequences for protein domain hits (default: no)
</p>
</dd>
<dt class="hdlist1">
<strong>-allchains</strong> [<em>yes|no</em>]
</dt>
<dd>
<p>
output features from all chains and unchained features, labeled with chain numbers (default: no)
</p>
</dd>
<dt class="hdlist1">
<strong>-maxgaplen</strong> [<em>value</em>]
</dt>
<dd>
<p>
maximal allowed gap size between fragments (in amino acids) when chaining pHMM hits for a protein domain (default: 50)
</p>
</dd>
<dt class="hdlist1">
<strong>-force_recreate</strong> [<em>yes|no</em>]
</dt>
<dd>
<p>
force recreation of hmmpressed profiles (default: no)
</p>
</dd>
<dt class="hdlist1">
<strong>-pbsmatchscore</strong> [<em>value</em>]
</dt>
<dd>
<p>
match score for PBS/tRNA alignments (default: 5)
</p>
</dd>
<dt class="hdlist1">
<strong>-pbsmismatchscore</strong> [<em>value</em>]
</dt>
<dd>
<p>
mismatch score for PBS/tRNA alignments (default: -10)
</p>
</dd>
<dt class="hdlist1">
<strong>-pbsinsertionscore</strong> [<em>value</em>]
</dt>
<dd>
<p>
insertion score for PBS/tRNA alignments (default: -20)
</p>
</dd>
<dt class="hdlist1">
<strong>-pbsdeletionscore</strong> [<em>value</em>]
</dt>
<dd>
<p>
deletion score for PBS/tRNA alignments (default: -20)
</p>
</dd>
<dt class="hdlist1">
<strong>-v</strong> [<em>yes|no</em>]
</dt>
<dd>
<p>
be verbose (default: no)
</p>
</dd>
<dt class="hdlist1">
<strong>-o</strong> [<em>filename</em>]
</dt>
<dd>
<p>
redirect output to specified file (default: undefined)
</p>
</dd>
<dt class="hdlist1">
<strong>-gzip</strong> [<em>yes|no</em>]
</dt>
<dd>
<p>
write gzip compressed output file (default: no)
</p>
</dd>
<dt class="hdlist1">
<strong>-bzip2</strong> [<em>yes|no</em>]
</dt>
<dd>
<p>
write bzip2 compressed output file (default: no)
</p>
</dd>
<dt class="hdlist1">
<strong>-force</strong> [<em>yes|no</em>]
</dt>
<dd>
<p>
force writing to output file (default: no)
</p>
</dd>
<dt class="hdlist1">
<strong>-seqfile</strong> [<em>filename</em>]
</dt>
<dd>
<p>
set the sequence file from which to take the sequences (default: undefined)
</p>
</dd>
<dt class="hdlist1">
<strong>-encseq</strong> [<em>filename</em>]
</dt>
<dd>
<p>
set the encoded sequence indexname from which to take the sequences (default: undefined)
</p>
</dd>
<dt class="hdlist1">
<strong>-seqfiles</strong> 
</dt>
<dd>
<p>
set the sequence files from which to extract the features
use <em>--</em> to terminate the list of sequence files
</p>
</dd>
<dt class="hdlist1">
<strong>-matchdesc</strong> [<em>yes|no</em>]
</dt>
<dd>
<p>
search the sequence descriptions from the input files for the desired sequence IDs (in GFF3), reporting the first match (default: no)
</p>
</dd>
<dt class="hdlist1">
<strong>-matchdescstart</strong> [<em>yes|no</em>]
</dt>
<dd>
<p>
exactly match the sequence descriptions from the input files for the desired sequence IDs (in GFF3) from the beginning to the first whitespace (default: no)
</p>
</dd>
<dt class="hdlist1">
<strong>-usedesc</strong> [<em>yes|no</em>]
</dt>
<dd>
<p>
use sequence descriptions to map the sequence IDs (in GFF3) to actual sequence entries.
If a description contains a sequence range (e.g., III:1000001..2000000), the first  part is used as sequence ID (<em>III</em>) and the first range position as offset (<em>1000001</em>) (default: no)
</p>
</dd>
<dt class="hdlist1">
<strong>-regionmapping</strong> [<em>string</em>]
</dt>
<dd>
<p>
set file containing sequence-region to sequence file mapping (default: undefined)
</p>
</dd>
<dt class="hdlist1">
<strong>-help</strong> 
</dt>
<dd>
<p>
display help for basic options and exit
</p>
</dd>
<dt class="hdlist1">
<strong>-help+</strong> 
</dt>
<dd>
<p>
display help for all options and exit
</p>
</dd>
<dt class="hdlist1">
<strong>-version</strong> 
</dt>
<dd>
<p>
display version information and exit
</p>
</dd>
</dl></div>
</div>
</div>
<div class="sect1">
<h2 id="_reporting_bugs">REPORTING BUGS</h2>
<div class="sectionbody">
<div class="paragraph"><p>Report bugs to <a href="https://github.com/genometools/genometools/issues">https://github.com/genometools/genometools/issues</a>.</p></div>
</div>
</div>
<div id="footer">
Copyright &copy; 2007-2023 The <i>GenomeTools</i> authors.
</div>
</div>
</body>
</html>
